BIOL 263: Molecular Biology and Genomics

Fall Semester 2005
Last modified Nov. 30, 2005
We are currently on schedule.
(Latest update overrides all previous versions, electronic and print.)

MWF 10:10 AM-11:00 AM (Period 3)
Tomsich Hall Room 101
(Owen York Lecture Hall)

Dr. Wade Powell
FSH 202, PBX 5396
Office hours: M 11 AM - noon and 3 - 4 PM; W, 11AM - 1 PM; F, 11AM - noon
(and by appointment)

The molecular and genomic basis of life is at the heart of modern biology. In BIOL 263, we will learn techniques and explore research questions at the forefront of molecular research, focusing on the mechanisms by which the information of the genome is expressed to form the functional molecules of living cells and organisms. The processes of DNA replication, recombination and repair, transcription of RNA from DNA templates, and translation of RNA into protein are discussed in the context of current research, frequently using primary literature. The function of genes and regulation and measurement of gene expression are treated in depth. Students analyze and publish interactive tutorials on the structure and function of key macromolecules. This intermediate-level course presumes a strong background in the basics of protein structure/function, central dogma processes, fundamental molecular techniques for manipulating nucleic acids and proteins, and general chemistry.
Required prerequisites: BIOL 113, 114; one year of chemistry; or permission of the instructor.
Recommended prerequisite or co-requisite: CHEM 231 and 232 (Organic Chemistry).

Reading Materials and Resources:

All reading assignments must be completed before class on the date indicated on syllabus.

Policies and Expectations:

Assignments and Grades: Your grade is based on performance in the following areas:

Important Links:
(Note: Some resources can only be accessed on Kenyon campus.)

Course Schedule

Day Date Topic Reading Notes Work Due
Part I: Molecular Interactions
M Aug 29 Course Introduction. DNA intro; 3D; B-DNA; A-RNA; DNA & RNA
W Aug 31 Weak bonds. Amino Acids; CAP; FAB; Ident Watson Ch 3; Ch 5, pp. 69-73    
F Sept 2 Adv DNA. FT; Z-DNA ; HIV; Triplex; Quad; base tautomers; supercoiling; Topo Watson Ch 6 Notes  
M Sept 5 AA2 in proteins. Ch 5 p 73-92; Notes  
W Sept 7

Introduction to crystallography methods; basic X-Ray;
more advanced X-Ray; crystallography terminology; Estrogen Receptor

basic X-ray; more advanced X-Ray (local version); another explanation (pdf). Notes  
F Sept 9 DNA-protein binding; Vocab; Human ADAR1;
ADAR activity and consequence
Schwartz 99;
Reading journal articles.
Part II: Gene Expression
M Sept 12 Transcription initiation
Structures: RnaPol-Bact; RnaPol-Euk
Watson Ch 12 pp. 347-363; Notes  
W Sept 14 Transcription Elongation; transcriptional road blocks
Structures: RnaPol-Bact; RnaPol-Euk
Epshtein & Nudler 2003    
F Sept 16

Bacterial Gene Regulation at level of transcription initiation. CAP-CTD ; Benoff
Cooperative binding

Watson Ch 16, pp. 483-504 Notes  
M Sept 19 Regulation of intiation, cont'd;
Regulation of events after initiation: Attenuation in E. coli.
Watson Ch 16, pp.504-511;
W Sept 21 Attenuation in Bacillus. TRAP-RNA;
Transcriptional regulation without regulatory proteins: Riboswitches.
Antson 99;
Watson Ch. 16, pp. 509-510; Soukup 2004
R Sept 22
4:00 PM
Seminar:  Dr. Kurt Fredrick, OSU Microbiology:  "Taking a Walk with the Ribosome"
    Higley Auditorium
F Sept 23 Catch-up day
Remarks about Monday's exam.
Points to ponder for the exam.
Breaker Lab Riboswitch site (Yale) & ppt movie Notes  
M Sept 26 Exam I (in class)      
W Sept 28 Eukaryotic Basal Transcription Factors. DAB PolII; TBP; TAF
Watson Ch. 12 pp.363-377;
Ch. 16, Box 16-1 (pp. 490-491).
F Sept 30 Eukaryotic Transcriptional Regulation; Spec. TFs. Activators; Identify
Watson Ch, 17, pp. 529-555; Notes  
M Oct 3 Eukaryotic Transcription, cont'd. . .  
W Oct 5 Nucleosomes & Transcriptional regulation; Histone Code. Figures; Nucleosome Watson Ch. 7 pp. 151-180; Ch. 17 p. 540 & pp. 556-562.
F Oct 7 Research in Eukaryotic Transcriptional Regulation: Histone acetyltransferase recruitment Sharma 2002
Chromatin IP
Remember PCR?
M Oct 10 October Reading Days; No Class      
W Oct 12 Transcript Splicing; Lupus; Splicing2; Spliceosome Watson Ch. 13 Notes  
F Oct 14 Translation initiation. Initiation. PDB Watson Ch. 14, pp. 411-439. Notes PDB Proposal
M Oct 17 Translation elongation, termination. Watson Ch. 14. pp. 440-459. Notes  
W Oct 19 Finish translation process;
"Protein Jive Sutra"
Watson Ch. 14.    
F Oct 21 Translation in the Nucleus? Notes
Nonsense-mediated decay
Iborra 01    
M Oct 24 RNA Interference
Animation from Nature Reviews Genetics .
Meister 04 (RNAi review paper)
Watson Ch. 17 pp. 567-570
W Oct 26 Argonaute in RNAi Liu 04
* supporting materials
F Oct 28 Exam II (points to ponder)      
Part III: DNA Replication, Repair, Recombination
M Oct 31 class cancelled      
W Nov 2 DNA Replication; Beta ring; DNA Rep; Replisome Watson Ch. 8 Notes  
F Nov 4 DNA Rep., cont'd.; Watson Ch. 8
M Nov 7 Mutation and repair. Watson Ch. 9 Notes Web Project Workshop 8-10 PM
W Nov 9 MutS; MutS-DNA; Figs. Obmolova 00    Web Project Workshop 8-10 PM
F Nov 11 Recombination; Experiments; RuvA; PNAS; Tn; Watson Ch. 10    
Part IV: Genomics
M Nov 14

Intro to Microarray Analysis (w/ Dr. Hicks)

(pdf version of slides)

Schulze 2001 review article
Watson Ch. 18, pp. 575-577
W Nov 16 Microarray Research: Diurnal & circadian related gene expression Schaffer 2001   Supplemental material
F Nov 18 Genomes: Human Genome; Ensembl
Black heart drug; Designer Babies
Watson Ch. 2, p. 38-39; Ch. 7, p. 133-138; Ch. 20, p. 660-671. Notes  
Nov 19-27 Thanksgiving Break      
Part V: Hot Topics
M Nov 28 Telomerase and telomeres Watson Ch. 8 p. 229-232.
Blackburn 2000 review
Notes Telomeres 12-mer; 22-mer
W Nov 30 Telomerase depletion and cancer cell division Li et al. 2005    
F Dec 2 Knockout mice in molecular biology

H19 Gene
Generation of Chimeras

M Dec 5 Exam Review      
W Dec 7 Exam III      
F Dec 9 Student Project Presentations     Completed Chime Tutorial
M Dec 12 Student Project Presentations      
Sat Dec 17 Revised Chime Tutorials Due No Broken Links   8:30 PM

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